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IMP Reference Guide  2.9.0
The Integrative Modeling Platform
IMP::npctransport::SlabWithPore Class Reference

#include <IMP/npctransport/SlabWithPore.h>

+ Inheritance diagram for IMP::npctransport::SlabWithPore:

Detailed Description

A decorator for a particle that represents a slab containing a cylindrical pore

Definition at line 23 of file SlabWithPore.h.

Public Member Functions

 SlabWithPore (::IMP::Model *m,::IMP::ParticleIndex id)
 
 SlabWithPore (const IMP::ParticleAdaptor &d)
 
void add_to_pore_radius_derivative (double v, DerivativeAccumulator &d)
 
Float get_pore_radius () const
 get cylindrical pore radius More...
 
bool get_pore_radius_is_optimized () const
 
Float get_thickness () const
 returns whether the particle last entered the transport moiety from its More...
 
void set_pore_radius (double r) const
 set cylindrical pore radius More...
 
void set_pore_radius_is_optimized (bool tf) const
 Set whether the coordinates are optimized. More...
 
void set_thickness (double thickness)
 sets slab thickness More...
 
void show (std::ostream &out=std::cout) const
 
- Public Member Functions inherited from IMP::Decorator
bool get_is_valid () const
 Returns true if constructed with a non-default constructor. More...
 
Modelget_model () const
 Returns the Model containing the particle. More...
 
Particleget_particle () const
 Returns the particle decorated by this decorator. More...
 
ParticleIndex get_particle_index () const
 Returns the particle index decorated by this decorator. More...
 
 operator Particle * () const
 
 operator ParticleIndex () const
 
Particleoperator-> () const
 

Static Public Member Functions

static bool get_is_setup (const IMP::ParticleAdaptor &p)
 
static bool get_is_setup (Model *m, ParticleIndex pi)
 Return true if the particle is an instance of SlabWithPore. More...
 
static FloatKey get_pore_radius_key ()
 Get the key for the pore radius. More...
 
static FloatKey get_thickness_key ()
 Get the decorator key for is_last_entry_from_top. More...
 
static SlabWithPore setup_particle (IMP::ParticleAdaptor decorator, double thickness, double pore_radius)
 
static SlabWithPore setup_particle (Model *m, ParticleIndex pi, double thickness, double pore_radius)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (ParticleAdaptor p)
 

Member Function Documentation

void IMP::npctransport::SlabWithPore::add_to_pore_radius_derivative ( double  v,
DerivativeAccumulator d 
)

add v to the derivative of the cylindrical pore radius, using derivative accumulator d

Definition at line 102 of file SlabWithPore.h.

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static bool IMP::npctransport::SlabWithPore::get_is_setup ( Model m,
ParticleIndex  pi 
)
static

Return true if the particle is an instance of SlabWithPore.

Definition at line 73 of file SlabWithPore.h.

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Float IMP::npctransport::SlabWithPore::get_pore_radius ( ) const

get cylindrical pore radius

Definition at line 91 of file SlabWithPore.h.

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static FloatKey IMP::npctransport::SlabWithPore::get_pore_radius_key ( )
static

Get the key for the pore radius.

Float IMP::npctransport::SlabWithPore::get_thickness ( ) const

returns whether the particle last entered the transport moiety from its

Definition at line 86 of file SlabWithPore.h.

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static FloatKey IMP::npctransport::SlabWithPore::get_thickness_key ( )
static

Get the decorator key for is_last_entry_from_top.

void IMP::npctransport::SlabWithPore::set_pore_radius ( double  r) const

set cylindrical pore radius

Definition at line 96 of file SlabWithPore.h.

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void IMP::npctransport::SlabWithPore::set_pore_radius_is_optimized ( bool  tf) const

Set whether the coordinates are optimized.

Definition at line 110 of file SlabWithPore.h.

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void IMP::npctransport::SlabWithPore::set_thickness ( double  thickness)

sets slab thickness

Definition at line 79 of file SlabWithPore.h.

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static SlabWithPore IMP::npctransport::SlabWithPore::setup_particle ( Model m,
ParticleIndex  pi,
double  thickness,
double  pore_radius 
)
static

Decorate a particle that represents a slab (e.g. nuclear envelope) with specified thickness and a cylindrical pore of specified pore_radius.

The slab is parallel to the x,y plain from z=-0.5*thickness to z=0.5*thickness, and the central axis of the pore lies on the origin.

Parameters
mthe model
pithe particle index
thicknessslab thickness
pore_radiuspore radius
Note
the pore radius is initially not optimizableSetup the particle so it can be used with this decorator.

Definition at line 70 of file SlabWithPore.h.


The documentation for this class was generated from the following file: